RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy14348
(225 letters)
>gnl|CDD|240302 PTZ00169, PTZ00169, ADP/ATP transporter on adenylate translocase;
Provisional.
Length = 300
Score = 300 bits (771), Expect = e-103
Identities = 133/218 (61%), Positives = 158/218 (72%), Gaps = 3/218 (1%)
Query: 1 MVDCFVRIPKEQGFGAYWRGNMANVIRYFPTQALNFAFKDKYKQIFLGGIDKSQFWAYFA 60
+V+CF R+ KEQG + WRGN ANVIRYFPTQA NFAFKD +K +F K+ FW +F
Sbjct: 55 IVNCFRRVSKEQGVLSLWRGNTANVIRYFPTQAFNFAFKDYFKNMFPKYNQKTDFWKFFG 114
Query: 61 GNLASGGAAGATSLCFVYPLDFARTRLGADVGKTGGAREFTGLGDCLTKIFKSDGIVGLY 120
N+ SGG AGA+SL VYPLDFARTRL +D+GK GG REFTGL DCL KI K G + LY
Sbjct: 115 VNILSGGLAGASSLLIVYPLDFARTRLASDIGK-GGDREFTGLFDCLMKISKQTGFLSLY 173
Query: 121 RGFGVSVQGIIIYRASYFGFFDTAKGML-PDPKNAGFLVSWGIAQVVTTVAGIVSYPFDT 179
+GFGVSVQGII+YR +YFG +D+AK +L + KN L W +AQ VT +AG++SYPFDT
Sbjct: 174 QGFGVSVQGIIVYRGAYFGLYDSAKALLFGNDKNTNILYKWAVAQTVTILAGLISYPFDT 233
Query: 180 VRRRLMMQSGR-GKSEIVYKGTLHCWAVIAKTEEQSNF 216
VRRR+MM SGR KSEI Y GTL CW I K E F
Sbjct: 234 VRRRMMMMSGRKAKSEIQYTGTLDCWKKILKNEGLGGF 271
Score = 47.5 bits (113), Expect = 1e-06
Identities = 44/170 (25%), Positives = 73/170 (42%), Gaps = 19/170 (11%)
Query: 59 FAGNLASGGAAGATSLCFVYPLDFARTRLGADVG----KTGGAREFTGLGDCLTKIFKSD 114
FA + GG + A S V P++ + + K+G ++G+ +C ++ K
Sbjct: 7 FATDFLMGGISAAISKTAVAPIERVKMLIQTQDSIPEIKSGKVPRYSGIVNCFRRVSKEQ 66
Query: 115 GIVGLYRGFGVSVQGIIIY---RASYFGFFDTAKGMLPD-PKNAGFLVSWGIAQVVTTVA 170
G++ L+RG + +I Y +A F F D K M P + F +G+ + +A
Sbjct: 67 GVLSLWRG---NTANVIRYFPTQAFNFAFKDYFKNMFPKYNQKTDFWKFFGVNILSGGLA 123
Query: 171 GIVS----YPFDTVRRRLMMQSGRGKSEIVYKGTLHCWAVIAKTEEQSNF 216
G S YP D R RL G+G + G C + K +Q+ F
Sbjct: 124 GASSLLIVYPLDFARTRLASDIGKGGDR-EFTGLFDC---LMKISKQTGF 169
Score = 45.9 bits (109), Expect = 6e-06
Identities = 32/123 (26%), Positives = 54/123 (43%), Gaps = 5/123 (4%)
Query: 1 MVDCFVRIPKEQGFGAYWRGNMANVIRYFPTQALNFAFKDKYKQIFLGGIDKSQFWAYFA 60
+ DC ++I K+ GF + ++G +V + F D K + G + +A
Sbjct: 156 LFDCLMKISKQTGFLSLYQGFGVSVQGIIVYRGAYFGLYDSAKALLFGNDKNTNILYKWA 215
Query: 61 GNLASGGAAGATSLCFVYPLDFARTRLGADVGKTGGAR-EFTGLGDCLTKIFKSDGIVGL 119
AG S YP D R R+ G+ + ++TG DC KI K++G+ G
Sbjct: 216 VAQTVTILAGLIS----YPFDTVRRRMMMMSGRKAKSEIQYTGTLDCWKKILKNEGLGGF 271
Query: 120 YRG 122
++G
Sbjct: 272 FKG 274
Score = 34.0 bits (78), Expect = 0.039
Identities = 15/42 (35%), Positives = 25/42 (59%), Gaps = 1/42 (2%)
Query: 3 DCFVRIPKEQGFGAYWRGNMANVIRYFPTQALNFAFKDKYKQ 44
DC+ +I K +G G +++G ANV+R AL F D+ ++
Sbjct: 257 DCWKKILKNEGLGGFFKGAWANVLRGA-GGALVLVFYDELQK 297
>gnl|CDD|215754 pfam00153, Mito_carr, Mitochondrial carrier protein.
Length = 96
Score = 93.1 bits (232), Expect = 1e-24
Identities = 36/97 (37%), Positives = 54/97 (55%), Gaps = 2/97 (2%)
Query: 56 WAYFAGNLASGGAAGATSLCFVYPLDFARTRLGADVGKTGGAREFTGLGDCLTKIFKSDG 115
F +L +GG AGA + YPLD +TRL + GG+R++ G+ DC KI+K +G
Sbjct: 2 PLSFLASLLAGGIAGAIAATVTYPLDVVKTRLQS--SAAGGSRKYKGILDCFKKIYKEEG 59
Query: 116 IVGLYRGFGVSVQGIIIYRASYFGFFDTAKGMLPDPK 152
I GLY+G ++ + A YFG ++T K +L
Sbjct: 60 IRGLYKGLLPNLLRVAPAAAIYFGTYETLKKLLLKKL 96
Score = 60.7 bits (148), Expect = 2e-12
Identities = 15/48 (31%), Positives = 28/48 (58%)
Query: 1 MVDCFVRIPKEQGFGAYWRGNMANVIRYFPTQALNFAFKDKYKQIFLG 48
++DCF +I KE+G ++G + N++R P A+ F + K++ L
Sbjct: 47 ILDCFKKIYKEEGIRGLYKGLLPNLLRVAPAAAIYFGTYETLKKLLLK 94
Score = 44.2 bits (105), Expect = 2e-06
Identities = 20/60 (33%), Positives = 27/60 (45%), Gaps = 2/60 (3%)
Query: 152 KNAGFLVSWGIAQVVTTVAGIVSYPFDTVRRRLMMQSGRGKSEIVYKGTLHCWAVIAKTE 211
FL S + +A V+YP D V+ RL + G + YKG L C+ I K E
Sbjct: 1 SPLSFLASLLAGGIAGAIAATVTYPLDVVKTRLQSSAAGGSRK--YKGILDCFKKIYKEE 58
>gnl|CDD|185494 PTZ00168, PTZ00168, mitochondrial carrier protein; Provisional.
Length = 259
Score = 36.8 bits (85), Expect = 0.005
Identities = 34/133 (25%), Positives = 57/133 (42%), Gaps = 27/133 (20%)
Query: 62 NLASGGAAGATSLCFVYPLDFARTRLGADVGKTGGAREFTGLGDCLTKIFKSDGIVGLYR 121
NL +G +G +YP+D +T + A K F I LY
Sbjct: 6 NLVTGALSGVIVDAVLYPIDSIKTNIQAK------------------KSFSFSDIKKLYS 47
Query: 122 GFGVSVQGIIIYRASYFGFFDTAKGMLPD-----PKNAGFLVSWGIAQVVTTVAGIVSYP 176
G ++ G + A ++ F++ +K +L + K +L+S IA++ A IV P
Sbjct: 48 GILPTLVGTVPASAFFYCFYELSKKLLTEYRENISKTNLYLISTSIAEI---TACIVRLP 104
Query: 177 FDTVRRRLMMQSG 189
F+ V++ M SG
Sbjct: 105 FEIVKQN-MQVSG 116
>gnl|CDD|239159 cd02758, MopB_Tetrathionate-Ra, The MopB_Tetrathionate-Ra CD
contains tetrathionate reductase, subunit A, (TtrA) and
other related proteins. The Salmonella enterica
tetrathionate reductase catalyses the reduction of
trithionate but not sulfur or thiosulfate. Members of
this CD belong to the molybdopterin_binding (MopB)
superfamily of proteins.
Length = 735
Score = 32.3 bits (74), Expect = 0.22
Identities = 18/68 (26%), Positives = 21/68 (30%), Gaps = 9/68 (13%)
Query: 133 YRASYFGFFDTAKGM---LPDPKNAGFLVSWGIAQVVTTVAGIVSYPFDTVRRRLMMQSG 189
YRA + G PD NA F + G T PF RRL
Sbjct: 188 YRAGNGALMNDLDGYPHVKPDFDNAEFALFIG------TSPAQAGNPFKRQARRLAEART 241
Query: 190 RGKSEIVY 197
G + V
Sbjct: 242 EGNFKYVV 249
>gnl|CDD|226857 COG4449, COG4449, Predicted protease of the Abi (CAAX) family
[General function prediction only].
Length = 827
Score = 30.0 bits (67), Expect = 1.2
Identities = 17/52 (32%), Positives = 23/52 (44%), Gaps = 6/52 (11%)
Query: 22 MANVIRYFPTQALNFAFKDKYKQIFL----GGIDKSQFWAYFAGNLASGGAA 69
+ VIR T+ L + Y Q++ G I SQ W +AGNL G
Sbjct: 393 LPKVIRDPFTEELQWEIP--YYQVYAHNPQGIIAGSQTWENYAGNLQRGWIQ 442
>gnl|CDD|238016 cd00059, FH, Forkhead (FH), also known as a "winged helix". FH
is named for the Drosophila fork head protein, a
transcription factor which promotes terminal rather
than segmental development. This family of
transcription factor domains, which bind to B-DNA as
monomers, are also found in the Hepatocyte nuclear
factor (HNF) proteins, which provide tissue-specific
gene regulation. The structure contains 2 flexible
loops or "wings" in the C-terminal region, hence the
term winged helix.
Length = 78
Score = 27.9 bits (63), Expect = 1.2
Identities = 9/20 (45%), Positives = 13/20 (65%), Gaps = 3/20 (15%)
Query: 3 DCFVRIPKE---QGFGAYWR 19
CFV++P+E G G+YW
Sbjct: 57 KCFVKVPREPDEPGKGSYWT 76
>gnl|CDD|237257 PRK12902, secA, preprotein translocase subunit SecA; Reviewed.
Length = 939
Score = 29.2 bits (66), Expect = 2.0
Identities = 14/34 (41%), Positives = 16/34 (47%)
Query: 92 GKTGGAREFTGLGDCLTKIFKSDGIVGLYRGFGV 125
G G R F L D L +IF D + GL F V
Sbjct: 676 GDPGSTRFFLSLEDNLLRIFGGDRVAGLMNAFRV 709
>gnl|CDD|239371 cd03073, PDI_b'_ERp72_ERp57, PDIb' family, ERp72 and ERp57
subfamily, second redox inactive TRX-like domain b';
ERp72 and ER57 are involved in oxidative protein
folding in the ER, like PDI. They exhibit both
disulfide oxidase and reductase functions, by
catalyzing the formation of disulfide bonds of newly
synthesized polypeptides and acting as isomerases to
correct any non-native disulfide bonds. They also
display chaperone activity to prevent protein
aggregation and facilitate the folding of newly
synthesized proteins. ERp57 contains two redox-active
TRX (a) domains and two redox inactive TRX-like (b)
domains. It shares the same domain arrangement of
abb'a' as PDI, but lacks the C-terminal acid-rich
region (c domain) that is present in PDI. ERp72
contains one additional redox-active TRX (a) domain at
the N-terminus with a molecular structure of a"abb'a'.
ERp57 interacts with the lectin chaperones, calnexin
and calreticulin, and specifically promotes the
oxidative folding of glycoproteins. ERp72 associates
with several ER chaperones and folding factors to form
complexes in the ER that bind nascent proteins. The b'
domain of ERp57 is the primary binding site and is
adapted for ER lectin association. Similarly, the b'
domain of ERp72 is likely involved in substrate
recognition.
Length = 111
Score = 27.7 bits (62), Expect = 2.2
Identities = 12/25 (48%), Positives = 15/25 (60%)
Query: 17 YWRGNMANVIRYFPTQALNFAFKDK 41
YWR + V + FP + LNFA DK
Sbjct: 35 YWRNRVLKVAKDFPDRKLNFAVADK 59
>gnl|CDD|189470 pfam00250, Fork_head, Fork head domain.
Length = 96
Score = 26.9 bits (60), Expect = 3.1
Identities = 7/20 (35%), Positives = 13/20 (65%), Gaps = 3/20 (15%)
Query: 3 DCFVRIPK---EQGFGAYWR 19
CF+++P+ + G G+YW
Sbjct: 57 KCFIKVPRSPDKPGKGSYWT 76
>gnl|CDD|214627 smart00339, FH, FORKHEAD. FORKHEAD, also known as a "winged
helix".
Length = 89
Score = 26.8 bits (60), Expect = 3.1
Identities = 10/19 (52%), Positives = 14/19 (73%), Gaps = 3/19 (15%)
Query: 3 DCFVRIPKE---QGFGAYW 18
DCFV++P+E G G+YW
Sbjct: 57 DCFVKVPREGDRPGKGSYW 75
>gnl|CDD|233212 TIGR00963, secA, preprotein translocase, SecA subunit. The
proteins SecA-F and SecY, not all of which are
necessary, comprise the standard prokaryotic protein
translocation apparatus. Other, specialized
translocation systems also exist but are not as broadly
distributed. This model describes SecA, an essential
member of the apparatus. This model excludes SecA2 of
the accessory secretory system [Protein fate, Protein
and peptide secretion and trafficking].
Length = 745
Score = 27.6 bits (62), Expect = 6.2
Identities = 14/34 (41%), Positives = 18/34 (52%)
Query: 92 GKTGGAREFTGLGDCLTKIFKSDGIVGLYRGFGV 125
G G +R F L D L +IF D + GL R G+
Sbjct: 505 GDPGSSRFFLSLEDNLMRIFGGDRLEGLMRRLGL 538
>gnl|CDD|200506 cd11245, Sema_plexin_B, The Sema domain, a protein interacting
module, of Plexin B. Plexins, which contain semaphorin
domains, function as receptors of semaphorins and may be
the ancestors of semaphorins. There are three members of
the Plexin B subfamily, namely B1, B2 and B3. Plexins
B1, B2 and B3 are receptors for Sema4D, Sema4C and
Sema4G, and Sema5A, respectively. The activation of
plexin B1 by Sema4D produces an acute collapse of axonal
growth cones in hippocampal and retinal neurons over the
early stages of neurite outgrowth and promotes branching
and complexity. By signaling the effect of Sema4C and
Sema4G, the plexin B2 receptor is critically involved in
neural tube closure and cerebellar granule cell
development. Plexin B3, the receptor of Sema5A, is a
highly potent stimulator of neurite outgrowth of primary
murine cerebellar neurons. Plexin B3 has been linked to
verbal performance and white matter volume in human
brain. Small GTPases play important roles in plexin B
signaling. Plexin B1 activates Rho through Rho-specific
guanine nucleotide exchange factors, leading to neurite
retraction. Plexin B1 possesses an intrinsic
GTPase-activating protein activity for R-Ras and induces
growth cone collapse through R-Ras inactivation. The
Sema domain is located at the N-terminus and contains
four disulfide bonds formed by eight conserved cysteine
residues. It serves as a ligand-recognition and -binding
module.
Length = 440
Score = 27.6 bits (61), Expect = 6.5
Identities = 13/41 (31%), Positives = 19/41 (46%), Gaps = 6/41 (14%)
Query: 51 DKSQFWAYFAGNLASGGAAGATSLCFVYPLD-----FARTR 86
K F + A ++ G ++LC +YPL F RTR
Sbjct: 260 GKVLFGVFSADEASTAAPDGRSALC-MYPLSSVDARFERTR 299
>gnl|CDD|213293 cd05927, LC-FACS_euk, Eukaryotic long-chain fatty acid CoA
synthetase (LC-FACS). The members of this family are
eukaryotic fatty acid CoA synthetases that activate
fatty acids with chain lengths of 12 to 20. LC-FACS
catalyzes the formation of fatty acyl-CoA in a two-step
reaction: the formation of a fatty acyl-AMP molecule as
an intermediate, and the formation of a fatty acyl-CoA.
This is a required step before free fatty acids can
participate in most catabolic and anabolic reactions.
Organisms tend to have multiple isoforms of LC-FACS
genes with multiple splice variants. For example, nine
genes are found in Arabidopsis and six genes are
expressed in mammalian cells.
Length = 539
Score = 27.5 bits (62), Expect = 7.3
Identities = 25/98 (25%), Positives = 33/98 (33%), Gaps = 19/98 (19%)
Query: 34 LNFAFKDKYKQIFLGGIDKSQFW---------AYFAGNLA---SGGAAGATSLCFVYPLD 81
NFA+ K + G S W A G + SGGA + +
Sbjct: 233 FNFAYNYKLAALRRGHGYASPLWDKLVFKKIKAALGGRVRLMLSGGAPLSPDT-----QE 287
Query: 82 FARTRLGADVGKTGGAREFTGLGDCLTKIF-KSDGIVG 118
F R LG V + G E G L+ + G VG
Sbjct: 288 FLRVALGCPVLQGYGLTETCA-GGTLSDPGDTTTGHVG 324
>gnl|CDD|235796 PRK06406, PRK06406, ribonucleotide-diphosphate reductase subunit
alpha; Validated.
Length = 771
Score = 27.5 bits (61), Expect = 7.5
Identities = 22/86 (25%), Positives = 33/86 (38%), Gaps = 18/86 (20%)
Query: 65 SGGAAGATSLCFVYPLD------FARTRLGADVGKTGGAREFTGLGDCLTKIFKSDGIVG 118
+G G S CFV P+ F + A + K+GG G G +++ D IV
Sbjct: 242 AGTKLGQLSACFVLPVPDSIEGIFNALKYTAMIHKSGG-----GTGFSFSRLRPKDDIVA 296
Query: 119 LYRGFGVSVQGIIIYRASYFGFFDTA 144
S +G+ S+ FD
Sbjct: 297 -------STKGVASGPLSFMRIFDVT 315
>gnl|CDD|204101 pfam08936, CsoSCA, Carboxysome Shell Carbonic Anhydrase.
Carboxysome Shell Carbonic Anhydrase is a bacterial
carbonic anhydrase localised in the carboxysome, where
it converts bicarbonate ions to carbon dioxide for use
in carbon fixation. It contains three domains, these
being: (1) an N-terminal domain composed primarily of
four alpha-helices; (2) a catalytic domain containing a
tightly bound zinc ion and (3) a C-terminal domain with
weak structural similarity to the catalytic domain.
Length = 459
Score = 27.2 bits (61), Expect = 7.7
Identities = 13/55 (23%), Positives = 22/55 (40%), Gaps = 11/55 (20%)
Query: 140 FFDTAKGMLPDPKNA-GFLVSWGIAQVVTT------VAGIVSY----PFDTVRRR 183
FF + FL+ G + T +A +++Y PF +VRR+
Sbjct: 92 FFADDPLWGQRAQAFESFLLECGFHLLDITPCADGRLAHLIAYVLRLPFSSVRRK 146
Database: CDD.v3.10
Posted date: Mar 20, 2013 7:55 AM
Number of letters in database: 10,937,602
Number of sequences in database: 44,354
Lambda K H
0.324 0.141 0.441
Gapped
Lambda K H
0.267 0.0768 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 11,821,515
Number of extensions: 1137904
Number of successful extensions: 1087
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1076
Number of HSP's successfully gapped: 32
Length of query: 225
Length of database: 10,937,602
Length adjustment: 93
Effective length of query: 132
Effective length of database: 6,812,680
Effective search space: 899273760
Effective search space used: 899273760
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.5 bits)
S2: 57 (25.7 bits)